If it's really the same problem, then it's not a surprise that those files don't exist, since the protXML file didn't get created, because the pepXML file never went through peptideProphet. But that doesn't quite sound like what you're describing - check the log to make sure of what's really going on.
Brian On Tue, Sep 22, 2009 at 1:02 AM, Melody Lam <[email protected]> wrote: > > Hi all! > > I have encountered the same problem. I am also using TPP v4.3.0 on > Windows XP. > > The output file "interact.prot.shtml" and the stylesheet > "interact.prot.xsl" files are not found in the directory of the input > file "interact.pep.xml". > However, by manually running the following line in the command prompt: > c:\Inetpub\tpp-bin\protxml2html.pl -file directory/interact.prot.xml > The output file interact.prot.shtml works as expected. > > I just wonder why throught the GUI the above command is not executed. > > Regards, > Melody > > > On Sep 18, 2:22 am, Brian Pratt <[email protected]> wrote: > > It appears to have never been run though peptideProphet. > > > > I should add a bit of logic to proteinProphet to catch that and issue a > more > > useful error message. > > > > On Thu, Sep 17, 2009 at 10:52 AM, Brian Pratt <[email protected] > >wrote: > > > > > I'll have a quick look at this. > > > > > Brian > > > > > On Thu, Sep 17, 2009 at 12:13 AM, YAN <[email protected]> > wrote: > > > > >> Hi everyone! > > >> Here are some more supplementary information from the output screen of > > >> TPP: > > > > >> Command 1 > > > > >> c:\Inetpub\tpp-bin\ProteinProphet c:/Inetpub/wwwroot/ISB/data/ > > >> probidoutput/ipimouse/interact.pep.xml c:/Inetpub/wwwroot/ISB/data/ > > >> probidoutput/ipimouse/interact.prot.xml > > > > >> > -------------------------------------------------------------------------------- > > > > >> Command FAILED > > > > >> Command 2 [Thu Sep 17 14:33:13 2009] [ Show / Hide ] > > > > >> c:\Inetpub\tpp-bin\protxml2html.pl -file > c:/Inetpub/wwwroot/ISB/data/ > > >> probidoutput/ipimouse/interact.prot.xml HTML > > > > >> > -------------------------------------------------------------------------------- > > > > >> ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the > > >> original Perl by A. Keller (TPP v4.3 JETSTREAM rev 0, Build > > >> 200908071234 (MinGW)) > > >> (xml input) (report Protein Length) (using degen pep info) > > >> . . . reading in c:/Inetpub/wwwroot/ISB/data/probidoutput/ipimouse/ > > >> interact.pep.xml. . . > > >> . . . read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with > > >> min prob 0.05 > > >> no data - quittingEND OUTPUT > > >> Writing results to html file: > c:/Inetpub/wwwroot/ISB/data/probidoutput/ > > >> ipimouse/interact.prot.html > > >> Command FAILED > > >> ................................................ > > > > >> I am running TPP on Windows XP and I just wonder why the program can't > > >> read the data from the pepxml file. > > >> I have also uploaded the pepXML file to this group at > > >>http://groups.google.com/group/spctools-discuss/web/yan.zip > > > > >> Thanks a lot! > > >> Yan > > > > --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected] To unsubscribe from this group, send email to [email protected] For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~----------~----~----~----~------~----~------~--~---
